algorithm.txt

- Example where
  - cost of alanine is being considered
  - in glucose limitation
  - at biomass flux of 0.5

- Set all exchange fluxes to have a lower bound of -10000.
  - Effectively unlimited nutrients with respect to biomass flux

- Set biomass flux reaction rate to have upper and lower bounds of 0.05

- Set glucose uptake reaction to be the model objective function
  - Objective function to be maximised as fluxes are negative for nutrients entering the cytoplasm

- Change alanine stoichiometry to 0.9998 of the value in the biomass reaction
  - Solve the model
  - Find flux through glucose intake reaction

- Repeat above step for alanine stoichiometry changes of 0.9998 - 1.0002

- Estimate the relative cost
  - Find the slope between changes in alanine stoichiometry (0.9998 - 1.0002) and glucose flux

- Estimate the absolute cost
  - relative cost * (100 / original alanine stoichiometry)

- Rescale fluxes independent of biomass flux
  - Divide both the relative and absolute cost estimates by 0.5 (the biomass flux)

units_of_cost.txt

Relative cost
-------------

Units of uptake (U) e.g. glucose, nitrogen, sulphur                         mmol-1 g-1 h-1

Units of percentage change in amino acid (%x) e.g. -0.0002% .. 0.0002%      unitless

Units of relative change of amino acid (dU/d%x)                             mmol-1 g-1 h-1

Units of growth rate (bio)                                                  h-1

Units of relative change rescaled by growth rate (dU/d%x) / bio             mmol-1 g-1
 

Absolute cost
-------------

Units of absolute amino acid stoichiometry (x0)                             mmol-1 g-1 ml-1

Relative cost rescaled by amino acid stoichiometry (dU/d%x) * (100/x0)      ml h-1

Units of growth rate (bio)                                                  h-1

Absolute cost rescaled by growth rate (dU/d%x) * (100/x0) / bio             ml